StarSolo 2.7.10b_alpha_220111, --soloCellReadStats Standard halts Solo running prematurely #1871
Description
Hi,
I am using a following Solo script;
#!/opt/homebrew/bin/zsh
index=/Volumes/MySlateDrive/star_genome_index/index_human_10x
whitelist=/Volumes/MySlateDrive/10X_Whitelist/737K-arc-v1.txt
r1=/Volumes/MySlateDrive/pbmc_granulocyte_sorted_3k/gex/pbmc_granulocyte_sorted_3k_S1_L003_R1_001.fastq.gz
r2=/Volumes/MySlateDrive/pbmc_granulocyte_sorted_3k/gex/pbmc_granulocyte_sorted_3k_S1_L003_R2_001.fastq.gz
r3=/Volumes/MySlateDrive/pbmc_granulocyte_sorted_3k/gex/pbmc_granulocyte_sorted_3k_S1_L004_R1_001.fastq.gz
r4=/Volumes/MySlateDrive/pbmc_granulocyte_sorted_3k/gex/pbmc_granulocyte_sorted_3k_S1_L004_R2_001.fastq.gz
STAR --genomeDir $index \
--runThreadN 40 \
--readFilesCommand 'gzip -c -d' \
--readFilesIn $r2,$r4 $r1,$r3 \
--soloCBwhitelist $whitelist \
--soloType CB_UMI_Simple \
--soloCBstart 1 \
--soloCBlen 16 \
--soloUMIstart 17 \
--soloUMIlen 12 \
--soloStrand Forward \
--soloBarcodeReadLength 0 \
--soloBarcodeMate 0 \
--clipAdapterType CellRanger4 \
--twopassMode Basic \
--soloMultiMappers EM \
--soloFeatures Gene GeneFull Velocyto \
--outFilterMultimapNmax 10 \
--outFilterScoreMin 30 \
--soloCBmatchWLtype 1MM_multi_Nbase_pseudocounts \
--soloUMIfiltering MultiGeneUMI_CR \
--soloUMIdedup 1MM_CR \
--soloCellFilter EmptyDrops_CR 5000 0.99 10 45000 90000 500 0.01 20000 0.01 10000 \
--outReadsUnmapped Fastx \
--outFileNamePrefix /Volumes/MySlateDrive/pbmc3Ksorted.GEX2 \
--outSAMtype None \
--soloCellReadStats Standard
The presence of --soloCellReadStats Standard parameter stops Solo at 1st pass mapping with no clear error message as in a following output;
STAR --genomeDir /Volumes/MySlateDrive/star_genome_index/index_human_10x --runThreadN 40 --readFilesCommand "gzip -c -d" --readFilesIn /Volumes/MySlateDrive/pbmc_granulocyte_sorted_3k/gex/pbmc_granulocyte_sorted_3k_S1_L003_R2_001.fastq.gz,/Volumes/MySlateDrive/pbmc_granulocyte_sorted_3k/gex/pbmc_granulocyte_sorted_3k_S1_L004_R2_001.fastq.gz /Volumes/MySlateDrive/pbmc_granulocyte_sorted_3k/gex/pbmc_granulocyte_sorted_3k_S1_L003_R1_001.fastq.gz,/Volumes/MySlateDrive/pbmc_granulocyte_sorted_3k/gex/pbmc_granulocyte_sorted_3k_S1_L004_R1_001.fastq.gz --soloCBwhitelist /Volumes/MySlateDrive/10X_Whitelist/737K-arc-v1.txt --soloType CB_UMI_Simple --soloCBstart 1 --soloCBlen 16 --soloUMIstart 17 --soloUMIlen 12 --soloStrand Forward --soloBarcodeReadLength 0 --soloBarcodeMate 0 --clipAdapterType CellRanger4 --twopassMode Basic --soloMultiMappers EM --soloFeatures Gene GeneFull Velocyto --outFilterMultimapNmax 10 --outFilterScoreMin 30 --soloCBmatchWLtype 1MM_multi_Nbase_pseudocounts --soloUMIfiltering MultiGeneUMI_CR --soloUMIdedup 1MM_CR --soloCellFilter EmptyDrops_CR 5000 0.99 10 45000 90000 500 0.01 20000 0.01 10000 --outReadsUnmapped Fastx --outFileNamePrefix /Volumes/MySlateDrive/pbmc3Ksorted.GEX2 --outSAMtype None --soloCellReadStats Standard
STAR version: 2.7.10b_alpha_220111 compiled: :/Users/akihikohoji/Downloads/Downloads/source
Jun 01 11:34:50 ..... started STAR run
Jun 01 11:34:50 ..... loading genome
Jun 01 11:35:28 ..... started 1st pass mapping
And a last part of log.out;
Sum of all Genome bytes: 5343458640
Sum of all SA bytes: 3109436257379
Sum of all SAi bytes: 185267190512
Processing splice junctions database sjdbN=362117, pGe.sjdbOverhang=100
alignIntronMax=alignMatesGapMax=0, the max intron size will be approximately determined by (2^winBinNbits)*winAnchorDistNbins=589824
Created thread # 1
Starting to map file # 0
mate 1: /Volumes/MySlateDrive/pbmc_granulocyte_sorted_3k/gex/pbmc_granulocyte_sorted_3k_S1_L003_R2_001.fastq.gz
mate 2: /Volumes/MySlateDrive/pbmc_granulocyte_sorted_3k/gex/pbmc_granulocyte_sorted_3k_S1_L003_R1_001.fastq.gz
Starting to map file # 0
mate 1: /Volumes/MySlateDrive/pbmc_granulocyte_sorted_3k/gex/pbmc_granulocyte_sorted_3k_S1_L003_R2_001.fastq.gz
mate 2: /Volumes/MySlateDrive/pbmc_granulocyte_sorted_3k/gex/pbmc_granulocyte_sorted_3k_S1_L003_R1_001.fastq.gz
Created thread # 2
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My system is as follows;
,xNMM. -----------------------------
.OMMMMo OS: macOS 13.4 22F66 arm64
OMMM0, Host: Mac13,2
.;loddo:' loolloddol;. Kernel: 22.5.0
cKMMMMMMMMMMNWMMMMMMMMMM0: Uptime: 3 hours, 28 mins
.KMMMMMMMMMMMMMMMMMMMMMMMWd. Packages: 208 (brew)
XMMMMMMMMMMMMMMMMMMMMMMMX. Shell: zsh 5.9
;MMMMMMMMMMMMMMMMMMMMMMMM: Resolution: 3440x1440
:MMMMMMMMMMMMMMMMMMMMMMMM: DE: Aqua
.MMMMMMMMMMMMMMMMMMMMMMMMX. WM: Quartz Compositor
kMMMMMMMMMMMMMMMMMMMMMMMMWd. WM Theme: Blue (Dark)
.XMMMMMMMMMMMMMMMMMMMMMMMMMMk Terminal: iTerm2
.XMMMMMMMMMMMMMMMMMMMMMMMMK. Terminal Font: Monaco 10
kMMMMMMMMMMMMMMMMMMMMMMd CPU: Apple M1 Ultra
;KMMMMMMMWXXWMMMMMMMk. GPU: Apple M1 Ultra
.cooc,. .,coo:. Memory: 3467MiB / 131072MiB